Extract Within-Group TCR Distance Vectors

For each level of splitField in the Seurat metadata, maps cells to their clone indices, subsets the clone-level distance matrix, and extracts the upper triangle as a flat numeric vector.

ExtractGroupDistanceVectors(
  seuratObj,
  assayName,
  splitField,
  minClonesPerGroup = 2,
  verbose = TRUE
)

Arguments

seuratObj

A Seurat object produced by CalculateTcrDistances (must have @misc$TCR_Distances).

assayName

Character. The distance assay to use (e.g., "TRA_fl", "TRB_cdr3", "TRA_TRB_fl").

splitField

Character. A metadata column name whose levels define the groups.

minClonesPerGroup

Integer. Minimum number of unique clones required in a group to produce a distance vector. Default 2.

verbose

Logical. Print progress messages. Default TRUE.

Value

A named list of numeric vectors, one per group level.